I believe they're trying to market to the general public. If Apple stores are good at turning heads from how they are designed, then it makes sense to apply that design to their own store. It's about getting people inside.
I see what you're saying, but don't you then run the risk of people not understanding what they're buying. It's ok selling it like an iphone, but if people are expecting an iphone, they're going to be disappointed.
Apple branding, stores and USP all kind of complement each other in that minimalist 'just works' feel. Raspi isn't that.
They don't care so long as they can spin it as the buyer's fault. Early on, before the Pi even launched, they encouraged grassroots marketing campaigns which (amongst other things) promoted the Pi as a consumer-y kind of home entertainment device. One of their forum members pointed out that this might lead to disappointment because it really wasn't a plug-and-play consumer device and required a certain amount of technical knowledge, and his concerns were roundly dismissed. Then after it launched, their staff complained that people who wrongly thought of it as some kind of consumer entertainment device were unfairly giving it a bad reputation because they didn't have the technical skills to get it working.